6-58275476-A-T

Variant names:

• chr6-58275476-A-T
• rs1850417
• ENST00000641631.1:n.291-25263A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000641631.1(ENSG00000225096):​n.291-25263A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.918 in 152,054 control chromosomes in the GnomAD database, including 64,216 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.92 (64216 hom., cov: 31)
• Consequence: ENSG00000225096 ENST00000641631.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549
• Publications: 2 publications found

Genes affected

ENSG00000225096 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641631.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225096	ENST00000641631.1		n.291-25263A>T		intron	N/A
	ENSG00000225096	ENST00000641775.1		n.456+112727A>T		intron	N/A
	ENSG00000225096	ENST00000661843.1		n.341-34820A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.917 AC: 139398 AN: 151936 Hom.: 64153 Cov.: 31

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.974

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.913

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.918 AC: 139520 AN: 152054 Hom.: 64216 Cov.: 31 AF XY: 0.917 AC XY: 68110 AN XY: 74314

African (AFR) AF: 0.982 AC: 40759 AN: 41526

American (AMR) AF: 0.916 AC: 13949 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3108 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5140 AN: 5146

South Asian (SAS) AF: 0.974 AC: 4696 AN: 4822

European-Finnish (FIN) AF: 0.848 AC: 8990 AN: 10598

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59779 AN: 67938

Other (OTH) AF: 0.914 AC: 1932 AN: 2114

Alfa AF: 0.870 Hom.: 2750

Bravo AF: 0.924

Asia WGS AF: 0.986 AC: 3426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.9
DANN	Benign	0.33
PhyloP100		0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1850417; hg19: chr6-58601754;